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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000315467
Querying Taster for transcript #2: ENST00000566566
MT speed 0 s - this script 7.607634 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GCSHpolymorphism_automatic2.18047802036381e-13simple_aaeaffectedS21Lsingle base exchangers8052579show file
GCSHpolymorphism_automatic2.18047802036381e-13simple_aaeaffectedS21Lsingle base exchangers8052579show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999782 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:81129822G>AN/A show variant in all transcripts   IGV
HGNC symbol GCSH
Ensembl transcript ID ENST00000315467
Genbank transcript ID NM_004483
UniProt peptide P23434
alteration type single base exchange
alteration region CDS
DNA changes c.62C>T
cDNA.187C>T
g.187C>T
AA changes S21L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS
21
frameshift no
known variant Reference ID: rs8052579
databasehomozygous (A/A)heterozygousallele carriers
1000G13599012260
ExAC81927
regulatory features Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Egr1, Transcription Factor, Egr1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Nrsf, Transcription Factor, Nrsf TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4680
0.360
(flanking)0.2520.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased196wt: 0.59 / mu: 0.73wt: CGCGGTCCCGTCACCCGCCGCGCCCTGCCCGCCGAGGCCCT
mu: CGCGGTCCCGTTACCCGCCGCGCCCTGCCCGCCGAGGCCCT
 ccgc|GCCC
Acc increased198wt: 0.33 / mu: 0.43wt: CGGTCCCGTCACCCGCCGCGCCCTGCCCGCCGAGGCCCTGG
mu: CGGTCCCGTTACCCGCCGCGCCCTGCCCGCCGAGGCCCTGG
 gcgc|CCTG
Donor marginally increased191wt: 0.9902 / mu: 0.9938 (marginal change - not scored)wt: TCACCCGCCGCGCCC
mu: TTACCCGCCGCGCCC
 ACCC|gccg
distance from splice site 87
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      21RALLCTLRAVPSPAAPCPPRPWQL
mutated  not conserved    21RALLCTLRAVPLPAAPCPPRPWQ
Ptroglodytes  all identical  ENSPTRG00000008386  21RALLCTLRGVPSPASPCPPRPWQ
Mmulatta  no alignment  ENSMMUG00000013088  n/a
Fcatus  no alignment  ENSFCAG00000013038  n/a
Mmusculus  not conserved  ENSMUSG00000034424  21RVVAYSLRTA---LTFCSPRPCV
Ggallus  no alignment  ENSGALG00000021019  n/a
Trubripes  no alignment  ENSTRUG00000017555  n/a
Drerio  no alignment  ENSDARG00000091655  n/a
Dmelanogaster  no alignment  FBgn0027945  n/a
Celegans  no alignment  D1025.2  n/a
Xtropicalis  not conserved  ENSXETG00000000187  23R-VLSTVTLVRRPAQECR-LVWR
protein features
start (aa)end (aa)featuredetails 
148TRANSITMitochondrion.lost
107107MOD_RESN6-lipoyllysine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 522 / 522
position (AA) of stopcodon in wt / mu AA sequence 174 / 174
position of stopcodon in wt / mu cDNA 647 / 647
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 126 / 126
chromosome 16
strand -1
last intron/exon boundary 550
theoretical NMD boundary in CDS 374
length of CDS 522
coding sequence (CDS) position 62
cDNA position
(for ins/del: last normal base / first normal base)
187
gDNA position
(for ins/del: last normal base / first normal base)
187
chromosomal position
(for ins/del: last normal base / first normal base)
81129822
original gDNA sequence snippet CACCCTGCGCGCGGTCCCGTCACCCGCCGCGCCCTGCCCGC
altered gDNA sequence snippet CACCCTGCGCGCGGTCCCGTTACCCGCCGCGCCCTGCCCGC
original cDNA sequence snippet CACCCTGCGCGCGGTCCCGTCACCCGCCGCGCCCTGCCCGC
altered cDNA sequence snippet CACCCTGCGCGCGGTCCCGTTACCCGCCGCGCCCTGCCCGC
wildtype AA sequence MALRVVRSVR ALLCTLRAVP SPAAPCPPRP WQLGVGAVRT LRTGPALLSV RKFTEKHEWV
TTENGIGTVG ISNFAQEALG DVVYCSLPEV GTKLNKQDEF GALESVKAAS ELYSPLSGEV
TEINEALAEN PGLVNKSCYE DGWLIKMTLS NPSELDELMS EEAYEKYIKS IEE*
mutated AA sequence MALRVVRSVR ALLCTLRAVP LPAAPCPPRP WQLGVGAVRT LRTGPALLSV RKFTEKHEWV
TTENGIGTVG ISNFAQEALG DVVYCSLPEV GTKLNKQDEF GALESVKAAS ELYSPLSGEV
TEINEALAEN PGLVNKSCYE DGWLIKMTLS NPSELDELMS EEAYEKYIKS IEE*
speed 1.60 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999782 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:81129822G>AN/A show variant in all transcripts   IGV
HGNC symbol GCSH
Ensembl transcript ID ENST00000566566
Genbank transcript ID N/A
UniProt peptide P23434
alteration type single base exchange
alteration region CDS
DNA changes c.62C>T
cDNA.83C>T
g.187C>T
AA changes S21L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS
21
frameshift no
known variant Reference ID: rs8052579
databasehomozygous (A/A)heterozygousallele carriers
1000G13599012260
ExAC81927
regulatory features Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Egr1, Transcription Factor, Egr1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
Nrsf, Transcription Factor, Nrsf TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
ZBTB7A, Transcription Factor, ZBTB7A Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4680
0.360
(flanking)0.2520.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased196wt: 0.59 / mu: 0.73wt: CGCGGTCCCGTCACCCGCCGCGCCCTGCCCGCCGAGGCCCT
mu: CGCGGTCCCGTTACCCGCCGCGCCCTGCCCGCCGAGGCCCT
 ccgc|GCCC
Acc increased198wt: 0.33 / mu: 0.43wt: CGGTCCCGTCACCCGCCGCGCCCTGCCCGCCGAGGCCCTGG
mu: CGGTCCCGTTACCCGCCGCGCCCTGCCCGCCGAGGCCCTGG
 gcgc|CCTG
Donor marginally increased191wt: 0.9902 / mu: 0.9938 (marginal change - not scored)wt: TCACCCGCCGCGCCC
mu: TTACCCGCCGCGCCC
 ACCC|gccg
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      21RALLCTLRAVPSPAAPCPPRPWQL
mutated  not conserved    21RALLCTLRAVPLPAAPCPPRPWQ
Ptroglodytes  all identical  ENSPTRG00000008386  21RALLCTLRGVPSPASPCPPRPWQ
Mmulatta  no alignment  ENSMMUG00000013088  n/a
Fcatus  no alignment  ENSFCAG00000013038  n/a
Mmusculus  not conserved  ENSMUSG00000034424  21RVVAYSLRTA---LTFCSPRPCV
Ggallus  no alignment  ENSGALG00000021019  n/a
Trubripes  no alignment  ENSTRUG00000017555  n/a
Drerio  no alignment  ENSDARG00000091655  n/a
Dmelanogaster  no alignment  FBgn0027945  n/a
Celegans  no alignment  D1025.2  n/a
Xtropicalis  not conserved  ENSXETG00000000187  23R-VLSTVTLVRRPAQECR-LVWR
protein features
start (aa)end (aa)featuredetails 
148TRANSITMitochondrion.lost
107107MOD_RESN6-lipoyllysine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 489 / 489
position (AA) of stopcodon in wt / mu AA sequence 163 / 163
position of stopcodon in wt / mu cDNA 510 / 510
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 22 / 22
chromosome 16
strand -1
last intron/exon boundary 314
theoretical NMD boundary in CDS 242
length of CDS 489
coding sequence (CDS) position 62
cDNA position
(for ins/del: last normal base / first normal base)
83
gDNA position
(for ins/del: last normal base / first normal base)
187
chromosomal position
(for ins/del: last normal base / first normal base)
81129822
original gDNA sequence snippet CACCCTGCGCGCGGTCCCGTCACCCGCCGCGCCCTGCCCGC
altered gDNA sequence snippet CACCCTGCGCGCGGTCCCGTTACCCGCCGCGCCCTGCCCGC
original cDNA sequence snippet CACCCTGCGCGCGGTCCCGTCACCCGCCGCGCCCTGCCCGC
altered cDNA sequence snippet CACCCTGCGCGCGGTCCCGTTACCCGCCGCGCCCTGCCCGC
wildtype AA sequence MALRVVRSVR ALLCTLRAVP SPAAPCPPRP WQLGVGAVRT LRTGPALLSV RKFTEKHEWV
TTENGIGTVG ISNFAQEALG DVVYCSLPEV GTKLNKQDEF GALESVKAAS ELYSPLSGEV
TEINEALAEN PGLVNKSCYE DGKLLLEISQ GITTTVNILS RI*
mutated AA sequence MALRVVRSVR ALLCTLRAVP LPAAPCPPRP WQLGVGAVRT LRTGPALLSV RKFTEKHEWV
TTENGIGTVG ISNFAQEALG DVVYCSLPEV GTKLNKQDEF GALESVKAAS ELYSPLSGEV
TEINEALAEN PGLVNKSCYE DGKLLLEISQ GITTTVNILS RI*
speed 1.60 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

Problems